Welcome!
The Single Cell & Transcriptomics Core will be CLOSED July 4 through July 6 for
sample submission. Please mark your calendar now and plan accordingly!
Effective 01/06/2023
RUSH options will not be available
If you have upcoming deadlines, please contact Linda Orzolek directly
to see if your timing needs can be met.
Join our NEW Single Cell list serve!
Email: sympa@lists.johnshopkins.edu with subject line: subscribe
SingleCell Firstname Lastname
Our aim is to provide cost-effective and time-efficient access to cutting-edge genomic technologies and expert assistance with experimental design and data analysis. The Core has been in continuous operation since 2002 and has supported research projects for more than 467 principal investigators, 1097 individual researchers, and processed more than 36,000 samples (as tallied in April 2016). We offer sample preparation and analysis using Next Generation & Third Generation sequencing technologies, Microarrays, Nanostring nCounter, and qPCR. We also offer high throughput DNA, Chromatin, and RNA shearing using the Covaris E220 system. Our lab is equipped with both PacBio and Oxford Nanopore platforms for third generation, long read, single-molecule real-time (SMRT) sequencing, as well as the Illumina NextSeq 500, MiSeq, and iSeq next-generation sequencer for short reads. We work closely with the ECGC to enable our clients access to the Illumina HiSeq 2500/3000 and NovaSeq for deeper sequencing requirements. The third-generation long-read sequencing technologies are great for genome assembly, novel transcript isoform identification, full-length 16s rRNA gene sequencing for metagenomics, repeat sequences, and GC-rich region targeted resequencing, as well as for bacterial DNA methylation study. The Illumina short-read sequencing technology, with its high throughput, is great for whole-genome resequencing, whole-exome sequencing, RNAseq, ChIPseq, 16s rRNA gene, or whole-genome metagenomic sequencing, and targeted DNA resequencing. We run the Affymetrix microarray system while offering preparation and support for Agilent arrays as well. In addition, we offer the Nanostring nCounter system for RNA expression, FFPE analysis, CNV, and miRNA detection. We ensure a full-service experience for our clients, starting with project design, all the way through publication. We encourage our clients to meet with us before beginning any projects to ensure the most accurate and efficient results. From nucleic acid extraction through analysis, we are your one-stop-shop.
Linda Orzolek, MS, Director
MRB Room 363
Office Phone: (410) 502-6658
Lab Phone: (443) 287-0262
Email: ldorsch2@jhmi.edu
Seth Blackshaw, Ph.D., Faculty Director
MRB Room 339
Email: sethblackshaw@gmail.com
| Hours | Location |
|
Hours Open: Monday - Friday 8:30am-5:00pm Hours Fully Staffed: Monday - Friday 8:30am-5:00pm |
733 N Broadway |
1. Transcriptomics and Deep Sequencing Core (hopkinsmedicine.org)
| Name | Role | Phone | Location | |
|---|---|---|---|---|
| Linda D. Orzolek, MS |
Director
|
410-502-6658
|
ldorsch2@jhmi.edu
|
MRB Room 359
|
| Seth Blackshaw, PhD |
Scientific Director
|
sethblackshaw@gmail.com
|
MRB Room 335
|
|
| Jasmeet Sethi, PhD |
Bulk Sequencing specialist
|
443-287-8852
|
jsethi1@jhmi.edu
|
MRB Room 355
|
| Conover Talbot Jr., BS |
Bioinformatician
|
410-614-0443
|
cct@jhmi.edu
|
MRB Room 353
|
| Tyler Creamer, PhD |
Single Cell Sequencing Specialist (RNA)
|
(443) 287-9056
|
tcreamer@jhmi.edu
|
MRB Room 363
|
| Jongseok Lee, PhD |
Single Cell Sequencing Specialist (DNA)
|
jlee243@jhmi.edu
|
MRB Room 360
|
| Price list |
| ► Data Analysis (3) | |||
| Name | Description | Price | |
|---|---|---|---|
| Core Computer/Software usage | Inquire | ||
| Data Analysis | Inquire | ||
| Ingenuity |
Usage of Ingenuity Pathway Analysis. This service requires user to register an account with Ingenuity. |
Inquire | |
| ► Library Prep (26) | |||
| Name | Description | Price | |
| 16S rRNA Library prep (1-16 samples) |
16S library prep, V3/V4, 1-16 samples |
Inquire | |
| 16S rRNA Library prep (17-48 samples) |
Metagenomic sequencing targeting 16s rRNA variable region 3 and 4. 17-48 samples. |
Inquire | |
| 16s rRNA Library prep (49+ samples) |
Metagenomic sequencing targeting 16s rRNA variable region 3 and 4. |
Inquire | |
| ATAC-seq library prep | Inquire | ||
| DNA/ChIP seq library preparation (96+) | Inquire | ||
| DNA/ChIPseq library preparation | Inquire | ||
| miRNA seq library prep | Inquire | ||
| Nextera | Inquire | ||
| Nextera (48+) | Inquire | ||
| Nextera (8+) | Inquire | ||
| small RNAseq library prep | Inquire | ||
| SMART-seq mRNA v4 library prep (non-stranded) | Inquire | ||
| SMART-seq mRNA v4 library prep (non-stranded) (24+) | Inquire | ||
| SMART-seq mRNA v4 library prep (non-stranded) (8+) | Inquire | ||
| SMART-seq mRNA v4 library prep (non-stranded) (96+) | Inquire | ||
| SMART-seq Total RNA v3 library prep | Inquire | ||
| SMART-seq Total RNA v3 library prep (24+) | Inquire | ||
| SMART-seq Total RNA v3 library prep (8+) | Inquire | ||
| SMART-seq Total RNA v3 library prep (96+) | Inquire | ||
| Stranded mRNA Seq library prep with UDI | Inquire | ||
| Stranded mRNA Seq library prep with UDI (8+) | Inquire | ||
| Stranded mRNA Seq library prep with UDI (96+) | Inquire | ||
| Stranded Total RNA Seq library prep with UDI | Inquire | ||
| Stranded Total RNA Seq library prep with UDI (24+) | Inquire | ||
| Stranded Total RNA Seq library prep with UDI (8+) | Inquire | ||
| Stranded Total RNA Seq library prep with UDI (96+) | Inquire | ||
| ► Nanostring (3) | |||
| Name | Description | Price | |
| DNA Assay | Inquire | ||
| Gene Expression Assay (12rxn) | Inquire | ||
| miRNA Assay | Inquire | ||
| ► Nucleic Acid Extraction (7) | |||
| Name | Description | Price | |
| Blue Pippin Size selection |
QC charges separate |
Inquire | |
| DNA extraction | Inquire | ||
| DNA extraction (12+) | Inquire | ||
| Nucleic Acid cleanup | Inquire | ||
| Nucleic Acid cleanup RUSH | Inquire | ||
| RNA extraction | Inquire | ||
| RNA extraction (12+) | Inquire | ||
| ► Quality Control (9) | |||
| Name | Description | Price | |
| QC only |
Do NOT complete for single cell sample or library QC. Please complete Single Cell sequencing request for all single cell library QC and/or sequencing. |
Inquire | |
| QC only (12+) | Inquire | ||
| QC with qPCR | Inquire | ||
| QC with qPCR (12+) | Inquire | ||
| QC with qPCR (RUSH) | Inquire | ||
| QC with qPCR (RUSH) (12+) | Inquire | ||
| qPCR only | Inquire | ||
| RUSH QC only | Inquire | ||
| RUSH QC only (12+) | Inquire | ||
| ► Sequencing (19) | |||
| Name | Description | Price | |
| iSeq 300 | Inquire | ||
| MiSeq 150 | Inquire | ||
| MiSeq 300 | Inquire | ||
| MiSeq 50 | Inquire | ||
| MiSeq 500 | Inquire | ||
| MiSeq 600 | Inquire | ||
| MiSeq Micro 300 | Inquire | ||
| MiSeq Nano 300 | Inquire | ||
| MiSeq Nano 500 | Inquire | ||
| NextSeq 500 High 150 |
NextSeq 500 sequencing using High Output 150 cycle reagents for single 150bp reads, or paired 75bp reads. Yield up to 400 million single/paired reads. |
JHU Internal
$4,100.00
each
|
|
| NextSeq 500 High 300 |
NextSeq 500 sequencing using High Output 300 cycle reagent kit for paired 150bp reads. Yield up to 400 million paired reads. |
JHU Internal
$5,800.00
each
|
|
| NextSeq 500 High 75 |
NextSeq 500 sequencing using High Output 75 cycle reagent kit for single 75bp reads. Yield up to 400 million reads. |
JHU Internal
$2,700.00
each
|
|
| NextSeq 500 Mid 300 (151-300bp) |
NextSeq 500 sequencing using Mid Output 300 cycle reagent kit for 300bp reads (any configuration). Yield upto 130 Million paired reads. |
Inquire | |
| NovaSeq S2 200 cycle (4.1B reads) | Inquire | ||
| NovaSeq S2 300 cycle (4.1B reads) | Inquire | ||
| NovaSeq S4 200 cycle (10B reads) | Inquire | ||
| NovaSeq S4 200 XP | Inquire | ||
| NovaSeq S4 300 cycle (10B reads) | Inquire | ||
| NovaSeq SP 200 cycle (800M reads) | Inquire | ||
| ► Shearing (4) | |||
| Name | Description | Price | |
| Covaris shearing | Inquire | ||
| Covaris shearing (10+) | Inquire | ||
| gTube Shearing | Inquire | ||
| gTube Shearing (10+) | Inquire | ||
| ► Single Cell Sequencing (32) | |||
| Name | Description | Price | |
| 10X 3' HT | Inquire | ||
| 10X 5' HT | Inquire | ||
| 10X 5' library prep-1st sample | Inquire | ||
| 10X 5' library prep-samples 2-7 | Inquire | ||
| 10X 5' VDJ enrichment |
T cell or B cell enrichment and library prep performed alongside 5' gene expression library. |
Inquire | |
| 10X ADT library (CITE-seq) | Inquire | ||
| 10X ATAC (2-7samples) | Inquire | ||
| 10X ATAC-seq | Inquire | ||
| 10X ATAC-seq (8+ samples) | Inquire | ||
| 10X ATAC-seq with Nuclei Isolation | Inquire | ||
| 10X Genomics Single Cell mRNA Library prep (8+) | Inquire | ||
| 10X Genomics Single Cell mRNA Library prep-1st sample |
10x Genomics Single cell mRNA sequencing to analyze 500-10,000 cells |
Inquire | |
| 10X Genomics Single Cell mRNA Library prep-samples 2-7 | Inquire | ||
| 10X HT service fee | Inquire | ||
| 10X multiome library prep (1st sample) | Inquire | ||
| 10X multiome library prep (8+) | Inquire | ||
| 10X multiome library prep (samples 2-7) | Inquire | ||
| 10X Single cell (labor only) | Inquire | ||
| CellenONE |
Hourly usage, requires training, self service only. Partial hours billed at full hourly rate |
Inquire | |
| CellRanger | Inquire | ||
| Custom reference genome creation | Inquire | ||
| Hashtag/MULTI-seq library prep | Inquire | ||
| MissionBio DNA+Protein library prep | Inquire | ||
| MissionBio sample prep |
MissionBio DNA library prep. Reagents provided by MissionBio. |
Inquire | |
| Parse Fixation kit |
Up to 4 reactions |
Inquire | |
| Parse Mega |
Parse single cell RNA combinatorial barcoding, up to 1 Million cells, up to 96 samples |
Inquire | |
| Parse WT |
Parse single cell RNA combinatorial barcoding, up to 100K cells, up to 48 samples |
Inquire | |
| Parse WT library prep only | Inquire | ||
| Parse-Mini |
Parse single cell RNA combinatorial barcoding, up to 10K cells, up to 12 samples |
Inquire | |
| Visium FFPE Package |
Includes reagents, library pre, sequencing & SpaceRanger Sectioning, staining and imaging NOT included |
Inquire | |
| Visium spatial fresh/frozen assay |
Library prep only Does not include cDNA amplification or QC |
Inquire | |
| Visium spatial fresh/frozen with cDNA amp |
Includes cDNA cycle number determination, amplification, QC and library prep |
Inquire | |
